Human gut microbial communities are among the most complex and diverse known, yet the contributionof differences in the composition of these communities to human health remains largely unexplored. Culture- independent 16S rRNA surveys have revealed large differences in the microbial communities amonghealthy adults. However, the strong selective pressure and influx of heterogeneous DNA in the gut provides an unparalleled opportunity for lateral gene transfer, so 16S rRNA may not tell us the whole story. Thus, understanding patterns of gene flow in the gut and relating 16S rRNA gene sequences to the rest of the genome is critical. In Project 3, we develop powerful new statistical tools for relating microbial communities in terms of the species, genes, transcripts, and metabolites they contain, and use these tools to provide the first quantitative estimates of the effects of host genetics and obesity to the composition of the human microbial community. Specifically, we will place species and genes in the human gut in context by relating them to the gut communities of a wide range of other mammals, and to community samples from hundreds of different physical environments ranging from oceans to soils. We will then use the distribution of species and genes related to those in the human gut to understand how the variability and diversity of gut communities within and between individuals relates to patterns observed in other species and environments. We will test the following two hypotheses. (1)There are systematic differences in human gut communities related to host genetics and to obesity. (2)The strong selective pressure in the gut environment results in adaptation through the acquisition of genes with specific functions, such as carbohydrate metabolism, through lateral gene transfer. We will examine these hypotheses by developing powerful new methods to detect lateral gene transfer, and by combining these methods with UniFrac,our tool for relating microbial communities. This project will utilize the community samples from monozygotic and dizygotic twins and their mothers from Project 1, and the pan-genome sequences of B. thetaiotaomicron and M. smithii from Project 2, to determine the relative contributions of genetic relatedness and obesity to the genes and species present in the gut communities ofindividual adult humans.